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annotate hicup_truncater.xml @ 7:cc413be789ea draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
author bgruening
date Thu, 23 Feb 2023 18:02:58 +0000
parents 30b199ed897d
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1 <tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@+galaxy0">
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2 <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
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3 <macros>
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4 <import>hicup_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_hicup"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 ##Dealing with inputs
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9 @PAIRED-END_INPUT@
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10
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11 hicup_truncater --re1 '$re1' --zip $advanced_options.nofill
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12 '$read1'
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13 '$read2'
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14 ]]></command>
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15 <inputs>
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16 <expand macro="input_paired"/>
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17 <expand macro="re1"/>
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18 <section name="advanced_options" title="Advanced options">
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19 <expand macro="no_fill"/>
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20 </section>
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21 </inputs>
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22 <outputs>
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23 <data name="dataset1_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 1 Output" from_work_dir="dataset1*.trunc.fastq.gz">
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24 <filter>library['type'] != 'paired_collection'</filter>
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25 </data>
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26 <data name="dataset2_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 2 Output" from_work_dir="dataset2*.trunc.fastq.gz">
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27 <filter>library['type'] != 'paired_collection'</filter>
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28 </data>
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29 <collection name="dataset_trunc_pairs" type="paired" format="fastq.gz" label="Hicup Truncation on ${on_string}">
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30 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
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31 <data name="forward" from_work_dir="dataset1*.trunc.fastq.gz"/>
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32 <data name="reverse" from_work_dir="dataset2*.trunc.fastq.gz"/>
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33 </collection>
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34 <data name="hicup_truncater_summary" format="tabular" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt"/>
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35 <collection type="list" name="truncation_barchart" label="Truncation Barchart.svg">
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36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.truncation_barchart\.svg$" directory="./" ext="svg"/>
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37 </collection>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <conditional name="library">
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42 <param name="type" value="paired"/>
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43 <param name="input_1" value="dataset1.fastq" ftype="fastq"/>
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44 <param name="input_2" value="dataset2.fastq" ftype="fastq"/>
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45 </conditional>
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46 <param name="re1" value="A^AGCTT"/>
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47 <output name="hicup_truncater_summary">
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48 <assert_contents>
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49 <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
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50 <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
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51 </assert_contents>
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52 </output>
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53 <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/>
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54 <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/>
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55 <output_collection name="truncation_barchart" count="2">
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56 <element name="dataset1.fq" file="dataset1.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
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57 <element name="dataset2.fq" file="dataset2.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
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58 </output_collection>
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59 </test>
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60 <test>
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61 <conditional name="library">
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62 <param name="type" value="paired_collection"/>
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63 <param name="input_1">
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64 <collection type="paired">
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65 <element name="forward" ftype="fastq" value="dataset1.fastq"/>
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66 <element name="reverse" ftype="fastq" value="dataset2.fastq"/>
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67 </collection>
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68 </param>
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69 </conditional>
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70 <param name="re1" value="A^AGCTT"/>
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71 <output name="hicup_truncater_summary">
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72 <assert_contents>
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73 <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
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74 <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
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75 </assert_contents>
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76 </output>
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77 <output_collection name="dataset_trunc_pairs" type="paired" count="2">
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78 <element name="forward" decompress="true" file="dataset1.trunc.fastq.gz" ftype="fastq.gz"/>
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79 <element name="reverse" decompress="true" file="dataset2.trunc.fastq.gz" ftype="fastq.gz"/>
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80 </output_collection>
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81 <output_collection name="truncation_barchart" count="2">
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82 <element name="dataset1.fq" file="dataset1.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
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83 <element name="dataset2.fq" file="dataset2.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
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84 </output_collection>
0
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88
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89 For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
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90
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91 To get more information about the truncater visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-truncater
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92 ]]></help>
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93 <expand macro="citation_hicup"/>
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94 </tool>